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Ribonucleotide Reductase Protein R1E from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLR poly-alanin model of ribonucleotide reductase protein R1 from E.coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 288 sodium malonate, magnesium chloride, DTT, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 4.42 72.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.99 α = 90 b = 98.99 β = 90 c = 291.488 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 Mirror 2001-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 43 100 0.12 0.12 15.7 11.1 24829 24829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.31 100 0.38 0.38 5.2 11.44
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT poly-alanin model of ribonucleotide reductase protein R1 from E.coli 3.2 43 23498 23498 1261 99.74 0.2061 0.2061 0.20376 0.2021 0.251 0.2479 RANDOM 40.666
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.82 -0.82 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.742 r_dihedral_angle_1_deg 4.59 r_scangle_it 3.848 r_scbond_it 2.166 r_angle_refined_deg 2.048 r_mcangle_it 1.736 r_angle_other_deg 1.024 r_mcbond_it 0.905 r_nbd_refined 0.319 r_nbd_other 0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.742 r_dihedral_angle_1_deg 4.59 r_scangle_it 3.848 r_scbond_it 2.166 r_angle_refined_deg 2.048 r_mcangle_it 1.736 r_angle_other_deg 1.024 r_mcbond_it 0.905 r_nbd_refined 0.319 r_nbd_other 0.283 r_symmetry_vdw_other 0.278 r_symmetry_hbond_refined 0.26 r_xyhbond_nbd_refined 0.202 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_other 0.172 r_chiral_restr 0.134 r_symmetry_hbond_other 0.077 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_nbtor_other 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5528 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing